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Layers and Groups are ways in which complex models can be separated into convenient bits.
After years of experience, our recommendations are these:

• Layers are better for pre-planned separation of significant parts of the model.
• Remember, entities belong to only one layer.  New entities are placed on the Active layer.  Copied entities are placed on the layer of the original entity (unless one un-checks that default option during the copy).
• If an entity (eg. a solid) belongs to one layer, whilst a different layer is Active, then if new feature operations are performed on the solid – like projecting, curve breaking, surface splitting etc. then the newly created entities will be on a different layer to the original.  Having entities on different layers and moving them onto the intended layer can be a bit inconvenient, which is why we suggest using a fairly small number of layers, where the Active Layer only changes during well defined sections of the modelling process.
• Double-clicking on a layer in the Model Info tree is the quickest way to change the Active layer.  A newly created layer is automatically the new Active Layer.
• Groups are another way to collect entities together, either for visualisation of complex models, or easy selection.  Entities can belong to multiple groups.
• Group | Operations | Generate… provides a variety of easy ways to separate small or large sections of a complex model using a variety of pre-defined methods.  Group | Operations | Automatic Add allows newly created entities to become part of the current (Active) group.
• The Grp button at the bottom right of the Femap window allows an easy switch between viewing the Full Model or the Active Group.
• Groups can be defined by rules (eg. elements that belong to some solids), or they can simply be a list of various entities.
• If there are very many groups and they are defined as large lists (eg. ID lists of 100,000 elements) rather than by association with a smaller list of geometry or properties etc,  then the saved model size can be much larger and a performance difference might be noticed.
• If groups get a little messy, it is easy to delete some (this only deletes the group, not the entities themselves), and recreate them as a tidier collection based on rules or Group Operations options.
•  A favourite of ours is Group | Operations | Generate Solids which groups a part of the model (elements, nodes, loads, contact regions etc.) based on association with one or multiple selected solids, including sheet solids.  This is useful also for viewing results, where the max-min scale of the contour legend will autoscale based on the elements/nodes grouped by this operation.